title: A Candida albicans PeptideAtlas.
abstract: Candida albicans public proteomic datasets, though growing steadily in the last few years, still have a very limited presence in online repositories. We report here the creation of a C. albicans PeptideAtlas comprising near 22,000 distinct peptides at a 0.24% False Discovery Rate (FDR) that account for over 2500 canonical proteins at a 1.2% FDR. Based on data from 16 experiments, we attained coverage of 41% of the C. albicans open reading frame sequences (ORFs) in the database used for the searches. This PeptideAtlas provides several useful features, including comprehensive protein and peptide-centered search capabilities and visualization tools that establish a solid basis for the study of basic biological mechanisms key to virulence and pathogenesis such as dimorphism, adherence, and apoptosis. Further, it is a valuable resource for the selection of candidate proteotypic peptides for targeted proteomic experiments via Selected Reaction Monitoring (SRM) or SWATH-MS.
  
  
  CONCLUSIONS
  This C. albicans PeptideAtlas resolves the previous absence of fungal pathogens in the PeptideAtlas project. It represents the most extensive characterization of the proteome of this fungus that exists up to the current date, including evidence for uncharacterized ORFs. Through its web interface, PeptideAtlas supports the study of interesting proteins related to basic biological mechanisms key to virulence such as apoptosis, dimorphism and adherence. It also provides a valuable resource to select candidate proteotypic peptides for future (SRM) targeted proteomic experiments. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
authors.affiliation: Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain. Electronic address: vvialasf@ucm.es.
authors.forename: Vital
authors.initials: V
authors.lastname: Vialas
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.
authors.forename: Carla Verónica
authors.initials: CV
authors.lastname: Loureiro y Penha
authors.affiliation: CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas, Spain.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Carrascal
authors.affiliation: CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Abián
authors.affiliation: Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.
authors.forename: Lucía
authors.initials: L
authors.lastname: Monteoliva
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain. Electronic address: conchagil@ucm.es.
authors.forename: Concha
authors.initials: C
authors.lastname: Gil
mesh_terms: D002176:Candida albicans / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000502:physiology; D040901:Proteomics
chemical_list: D005656:Fungal Proteins
keywords: CGD; Candida Genome Database; Candida albicans; ESS; Empirical Suitability Score; FDR; False Discovery Rate; PRIDE; PSM; PSS; PeptideAtlas; Peptide–Spectrum Match; Predicted Suitability Score; Protein Identifications Database; Proteotypic peptides; SRM; Selected Reaction Monitoring